Similar regions between promoters of ysdA

>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub CATGAAATCTGGAAACTATGCTTTCCGTGACCGTCGTCAGAAAAAACGTGATTTCCGTAA hal .............AACAATGGTTTTATTGA.............................. ste ................TATGCGTATCGCGACCGCCGTCAACGGAAGCGCGACTTCCGCAA -300 -290 -280 -270 -260 -250 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub ACTTTGGATCACTCGTATCAACGCAGCTGCTCGCATGAACGGCCTTTCTTACAGCCGTTT hal ...................AACGAAGGTGATCAAGAGAAACGCCTTT...ACAATGGTTT ste ACTGTGGATTGTCCGCATCAACGCAGCGGCTCGCCAAAATGGCTTGTCCTACAGCCGTTT -240 -230 -220 -210 -200 -190 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub AATGCACGGTCTTAAGCTTTCTGGTATCGAAGTAAACCGTAAAATGCTTGCTGATCTTGC hal TATTGAAGGGCTGAA.......GTTTTCGAAGGAGGCTGTACA................. ste GATGCACGGCTTGAAGCTGGCCGGCGTGGAAGTGAACCGGAAAATGCTCGCCGACTTGGC -180 -170 -160 -150 -140 -130 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sub TGTAAACGATCTTACTGCATTCAATCAGCTTGCTGATGCTGCTAAAGCTCAATTAAACAA hal .............ACCGCATTCTATTA............TGCGAAACCGCATTCTATTAC ste GGTGAACGACCAAGCCGCGTTCGCCCAACTCGCCGACTTGGCGAAAGCGAATTTGAATAA -120 -110 -100 -90 -80 -70 >>>> ]]]]]]]]]]]]]]]]]]]]] sub GTAATCATATAGAGCCGCTCTCCAGCAGAGCGGCTTTTTCTATATAAAGGATGAGGCAAC hal ATCATCA..........................CTTTTTC-ATTGGAAGAAGGAG..... ste ATAA-CAACGATGGCCATCCTTGATCAGGGTGGCCATTTTCTTATCAAGGA......... -60 -50 -40 -30 -20 -10 -1 > : other CDS - : gaps within a similar region ] : terminator . : gaps between similar regions } : RNAs @ : known binding sites <,[,{ : opposite direction About alignment...